This just in. Current Biology has published a short dispatch piece reviewing the flagellum evolution issue:

W. Ford Doolittle and Olga Zhaxybayeva (2007). “Reducible Complexity - The Case for Bacterial Flagella.” Current Biology, 17(13), R510-R512. July 3, 2007. DOI

I recently expressed some discouragement about the capabilities of blogs for critiquing scientific papers. I still have those reservations, but here is a data point that leans the other way:

A correction to the paper by Liu & Ochman, “Stepwise formation of the bacterial flagellar system,” was just published in PNAS. PT readers will recall that I and others had many problems with the methods and conclusions of this paper (see PT posts 1, 2, 3 for commentary and 4 for comprehensive links). The correction and brief comments are below.

For you flagellum wonks in the audience, an interesting and fairly detailed discussion of some of the science issues and, for lack of a better word, etiquette issues, took place over here at T. Taxus in “JCVI Evolutionary Genomics Journal Club on Liu-Ochman.”

(The discussion is also good for Esperanto wonks.)

The PNAS Early Edition webpage has just posted a series of papers from the December 2006 National Academy of Sciences Sackler Colloquium, “In the Light of Evolution: Adaptation and Complex Design,” organized by Francisco Ayala and John Avise. The series of papers, on topics ranging from color vision to beetle horns, is now available (I will post the list below the fold). Eugenie C. Scott (aka Genie) was invited to speak at this meeting about evolution education and the history of opposition to it, and the speakers wrote papers to be published in PNAS and a forthcoming NAS volume.

Genie brought me on as a coauthor on the paper she was asked to write. This became:

As the discussion over the Liu-Ochman flagellum evolution paper continues, it is clear that I need to do a little more arguing to defend my position. Although some were convinced that skepticism was justified based the previous PT posts (basically: 1. this goes against much prior published knowledge and 2. just look at the obviously different structures), others have defended the paper or at least suggested that the alleged problems are not as overwhelmingly obvious as they seem to me. Two primary lines of argument have been raised. First, some have pointed out, correctly, that the reputation of the authors and journal in question far outweighs the reputation of a blogger like me, so why should readers trust me over PNAS? I will concede the case when it comes to reputation; all I can say is that over the years I have developed some familiarity with the literature pertinent to flagellum evolution, and as I read through the PNAS paper it became apparent that it was going against much of what was already known. This is not necessarily bad if a direct attempt is made to rebut conventional wisdom, but if assertions are made without much evidence of awareness that they go against previous work, that is problematic.

Those who have been following the comments section of the first post on the PNAS flagellum paper, entitled “Stepwise formation of the bacterial flagellar system,” will see that there have been several developments: ScienceNOW at Science magazine has uncritically reported the PNAS paper’s all-flagellar-genes-came-from-one conclusion; Behe and other IDers are getting into the act, although they are so clueless they don’t really even understand why the PNAS paper is problematic; and PZ Myers and I have dropped hints that several of us PT bloggers are reaching the conclusion that this paper is looking worse, not better, after close examination. We will have more on the technical methodology issues in the next few days. For the moment I would just like to offer a simple response to some comments, and a simple but powerful reason that the “all core flagellum genes are descended from one ancestral gene” does not work.

First, the comments. Some commentators have reacted along the following lines: (1) maybe the paper isn’t so bad, just speculative; and/or (2) maybe I’ve misread the paper or its conclusion was poorly worded, and maybe the authors just meant to argue that some of the 24 core flagellar proteins were related, not all 24 proteins.

Unfortunately – and I mean unfortunately because I wish one of these options was true – neither idea is a supportable interpretation of the authors’ views. Have another look at Figure 3 from the Liu & Ochman paper:

Today the prestigious journal Proceedings of the National Academy of Sciences (PNAS) put out an Advanced Online Publication paper on flagellum evolution entitled, “Stepwise formation of the bacterial flagellar system.” The paper is freely available via Open Access. I was initially excited that PNAS had published a paper on this topic, and furthermore that it cited the Pallen/Matzke essay on flagellum evolution, and Ian Musgrave’s excellent book chapter in Why Intelligent Design Fails.

Unfortunately, as I read the paper, my delight turned to concern, and then dismay. The paper makes some potentially useful points and explores new territory in a few areas. But much of it ranges from dubious to just irremediably wrong.

I was recently interviewed by Karl Mogel for his podcast show The Inoculated Mind. Topics include flagellum evolution and Kitzmiller v. Dover, and Casey Luskin’s inability to admit error. Have a listen if you get a chance.

A few weeks back, I posted a rebuttal to the Casey Luskin/Michael Behe interview, which itself rebutted the Pallen/Matzke Nature Reviews Microbiology paper on flagellum evolution.

Over on the hopefully-named “ID the Future” podcast website run by the Discovery Institute, Casey Luskin has posted a short interview with Michael Behe – evidently recorded in-studio rather than over the phone, although, for some reason, Behe sounds like he is sitting in a cave.

Anyway, the topic of the interview is Behe’s response to the Pallen and Matzke (2006) article on flagellum evolution in Nature Reviews Microbiology. As I pointed out on PT last month, among other things, the NRM article showed that the ID advocates didn’t know what they were talking about on the topics of (1) number of required flagellum parts, and (2) number of “unique”, i.e. non-homologous, flagellum parts. These points are obviously important, since the ID advocates themselves have emphasized them repeatedly – almost in hypnotically repetitious fashion, actually – as major reasons that the flagellum could not have evolved gradually.

Carl Zimmer has a post up about his new article in the November 2006 issue of National Geographic. The article surveys recent research on the origin of multicellularity, segmentation, the vertebrate head, eyes, limbs, feathers, flowers, and the new kid on the block…the flagellum! And he even bases it on Pallen and Matzke 2006. Mark Pallen is interviewed – unfortunately there is nothing about the Genomic Dub Collective, but I’m sure that’s destined for ReggaeTimes.

Famed flagellum researcher Howard Berg is also interviewed. Sadly, there is nothing about the ID movement’s frequent claim that one of the spiffy design features of the flagellum is that it is “water-cooled” – a claim which they usually attribute to Berg (googling “water-cooled flagellum” brings up only ID/creationism websites). In my humble opinion, a fish has a far stronger claim to being “water-cooled”, given that the heat-retention capabilities of nanometer-scale molecular system are essentially nil (I read once that the heat energy radiates away dissipates in picoseconds at that scale). Someone should ask him about that some day.

I want one of these for Christmas. Courtesy of Display #1: The Bacterial Flagellum, at the Creation Science Museum of Canada. Watch out, evolutionists, you have been judged on the Hogwash-O-Meter and found wanting! If that doesn’t convince you, just look at the tracks of humans found with dinosaur tracks at Paluxy.

Anyone who has been a “creationism watcher” for any length of time is familiar with the venerable creationist tactic of “quote mining.” Since creationists, essentially universally, can’t (or don’t want to) deal with actual scientific data pertaining to evolution, they attempt maintain a facade of respectibility by quoting statements from biological authorities. This can take many forms; for example, for the 1987 Supreme Court Edwards v. Aguillard case, the creationist lawyer Wendell Bird, apparently with the help of Paul Nelson, assembled a massive 500-page brief that consisted almost entirely of thousands of quotes from authorities on every topic bearing on “creation science”, from astrophysics to biology to philosophy to religion. This failed to convince the Supremes, but Bird turned his brief into a large two-volume book, The Origin of Species Revisited. Other elaborations on creationist quote-mining include various “Quote Books”, including The Quote Book (1984 booklet, inserted in Creation magazine I believe) and The Revised Quote Book (1990) from Answers in Genesis, the Handy Dandy Evolution Refuter (now online), and Henry Morris’ That Their Words may be used against Them (comes with CD!). Then we have endless collections of quotes on creationist websites, 50 of which were recently surveyed and ranked against the Talk.Origins Quote-Mine Project. Sometimes these quotes evolve and mutate over time (here is an example from Of Pandas and People), and sometimes they even spontaneously generate from thin air, as with this imaginary quote from Clarence Darrow.

You may be saying, “Surely this is a problem, but only famous authorities get quote mined. It would never happen to me!” Think again. On September 5, 2006, an article I coauthored in Nature Reviews Microbiology on flagellum evolution was published on the NRM website as an Advanced Online Publication. Before the ink was even dry – heck, before the ink was even wet, the October issue hasn’t come out yet – Casey Luskin at the Discovery Institute is quote mining it! The mining occured in Luskin’s insta-response to the revised edition Chris Mooney‘s book The Republican War on Science. Check this out:

Jonathan Wells (2006) The Politically Incorrect Guide to Darwinism and Intelligent Design. Regnery Publishing, Inc. Washington, DC.^Amazon

Read the entire series.

No book on “intelligent design” would be complete without a mention of the concept of irreducible complexity. Jonathan Wells’s The Politically Incorrect Guide to Darwinism and Intelligent Design does not disappoint in this regard; it is the actual discussion of irreducible complexity that is very disappointing and down right misleading.

When I returned from vacation today, I was surprised to discover this new article pop up in my automated searches for flagellum stuff in the literature databases:

Pallen MJ, Matzke NJ. (2006). “From The Origin of Species to the origin of bacterial flagella.” Nature Reviews Microbiology, 4(10), 784-790. October 2006. Advanced Online Publication on September 5, 2006. [PubMed] [Journal] [DOI] [Google Scholar]

In the recent Dover trial, and elsewhere, the ‘Intelligent Design’ movement has championed the bacterial flagellum as an irreducibly complex system that, it is claimed, could not have evolved through natural selection. Here we explore the arguments in favour of viewing bacterial flagella as evolved, rather than designed, entities. We dismiss the need for any great conceptual leaps in creating a model of flagellar evolution and speculate as to how an experimental programme focused on this topic might look.

Matzke NJ? Hey, I know that guy!

I thought that this article was not coming out until October, and I would therefore have a few weeks to prepare some suitable PT posts to update everyone on developments in flagellar evolution since my first effort in 2003 (read this for background), and on the litany of errors and pseudoscience that the ID movement has produced regarding their favorite “Icon of Intelligent Design.” But, the powers that be at Nature Reviews Microbiology have seen fit to release the article as an Advanced Online Publication – and put it on their front page, no less – so it remains a secret no longer. C’est la vie.

There are several large flagellum-related topics I still plan to blog in the near future, but for the moment I would just like to hit one topic: what is The Main Point that PT readers should get out of the article?

A paper that just came out in Advance Online Publication section of Nature, Murphy et al. 2006, reports the first in situ structure of a flagellar motor in a spirochete, Treponema primitia. Such things have been done before, for the bacterial lab rat Salmonella, but spirochetes are a whole different bacterial phylum, and they have weird flagella. First, instead of the flagella sticking outside of the cell and doing what any self-respecting flagellum would do, the flagella of spirochetes rotate entirely within the periplasm (the space between the inner and outer membrane, which includes the cell wall). You might think that there would be no room for the flagellum to rotate in such a restricted space, or that it would tear apart the membranes – but intuitions are very unreliable at the sub-microscopic scale. The intracellular rotation of the flagella evidently cause the whole cell to gyrate, moving it through liquid in a corkscrew-like fashion.

It seems that Dembski has decided to ‘decisively’ move the goalposts of ID further out and although in earlier writings he did mention the possibility of ‘front loading’, he also considered such possibilities to be unlikely and ‘deistic’ in nature.

Now he may have clarified his position:

Dembski wrote:

Let’s cut to the chase: Is the designer responsible for biological complexity God? Even as a very traditional Christian and an ardent proponent of ID, I would say NOT NECESSARILY. To ask who or what is the designer of a particular object is to ask for the immediate intelligent agent responsible for its design. The point is that God is able to work through derived or surrogate intelligences, which can be anything from angels to organizing principles embedded in nature.

For instance, just because I hold to both Christian theism and ID doesn’t mean that God directly designed and implemented the bacterial flagellum by specifically toggling its components. It could well have happened by a process of natural genetic engineering of the sort envisioned by James Shapiro. The design would be no less real, but God’s role in the design would be distant, not proximal.

Philosophers have long distinguished between primary and secondary causes. The problem is that under the pall of methodological naturalism, secondary causes have been identified with purely materialistic processes. But it’s perfectly legitimate for secondary causes to include teleological processes. I develop all this at length in THE DESIGN REVOLUTION.

Anything from angels to organizing principles, I clearly see the scientific value of ID here. And the logical conclusion from Dembski’s admissions about front-loading is that natural explanations would be able to explain the origin of such features as the bacterial flagellum. Thus, lacking any further evidence, science would be unable to reach a conclusion of ‘intelligent design’ as the evidence would be hidden beyond our observations. In other words, Intelligent Design has moved itself further into the realm of scientific vacuity.

Not bad for a days work though. Boy do I wish Dembski had testified at the Dover trial.

I find it fascinating that Dembski on the one hand seems to be arguing that complex specified information requires a supernatural origin while on the other hand arguing that CSI can in fact be explained by natural law alone. Whether or not a supernatural designer was responsible for the front loading is a question science cannot answer.
Which is exactly why Intelligent Design makes for poor science and good apologetics. As such, I start to understand more and more why Dembski has returned to apologetics.

Given the recent scientific progress, it may not come as a surprise to see ID proponents retreat to front-loading.